Starting phenix.real_space_refine on Wed Mar 4 06:05:19 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7kcm_22816/03_2026/7kcm_22816.cif Found real_map, /net/cci-nas-00/data/ceres_data/7kcm_22816/03_2026/7kcm_22816.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.43 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7kcm_22816/03_2026/7kcm_22816.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7kcm_22816/03_2026/7kcm_22816.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7kcm_22816/03_2026/7kcm_22816.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7kcm_22816/03_2026/7kcm_22816.map" } resolution = 3.43 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 522 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 8 Type Number sf(0) Gaussians K 2 8.98 5 Fe 2 7.16 5 P 6 5.49 5 Mg 2 5.21 5 S 55 5.16 5 C 6845 2.51 5 N 1883 2.21 5 O 2043 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 67 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10838 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 4890 Number of conformers: 1 Conformer: "" Number of residues, atoms: 612, 4890 Classifications: {'peptide': 612} Link IDs: {'PTRANS': 18, 'TRANS': 593} Chain breaks: 3 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "B" Number of atoms: 4915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 614, 4915 Classifications: {'peptide': 614} Link IDs: {'PTRANS': 18, 'TRANS': 595} Chain breaks: 3 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "C" Number of atoms: 963 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 963 Classifications: {'peptide': 121} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 7, 'TRANS': 113} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' K': 1, ' MG': 1, 'ANP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' K': 1, ' MG': 1, 'ANP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 10324 SG CYS C 101 61.372 22.904 42.313 1.00137.29 S ATOM 10403 SG CYS C 113 61.826 21.691 38.704 1.00144.04 S ATOM 10270 SG CYS C 93 58.230 17.757 41.308 1.00147.05 S ATOM 10308 SG CYS C 98 57.052 20.959 43.032 1.00140.48 S Time building chain proxies: 2.60, per 1000 atoms: 0.24 Number of scatterers: 10838 At special positions: 0 Unit cell: (96.866, 91.982, 130.24, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Fe 2 26.01 K 2 19.00 S 55 16.00 P 6 15.00 Mg 2 11.99 O 2043 8.00 N 1883 7.00 C 6845 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.69 Conformation dependent library (CDL) restraints added in 530.8 milliseconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES C 201 " pdb="FE2 FES C 201 " - pdb=" SG CYS C 98 " pdb="FE1 FES C 201 " - pdb=" SG CYS C 113 " pdb="FE1 FES C 201 " - pdb=" SG CYS C 101 " pdb="FE2 FES C 201 " - pdb=" SG CYS C 93 " Number of angles added : 6 2658 Ramachandran restraints generated. 1329 Oldfield, 0 Emsley, 1329 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2568 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 14 sheets defined 44.2% alpha, 18.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.26 Creating SS restraints... Processing helix chain 'A' and resid 93 through 104 removed outlier: 3.632A pdb=" N LEU A 97 " --> pdb=" O GLU A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 110 through 135 removed outlier: 4.326A pdb=" N ARG A 114 " --> pdb=" O GLU A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 172 Processing helix chain 'A' and resid 178 through 186 removed outlier: 3.780A pdb=" N ALA A 182 " --> pdb=" O SER A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 210 Processing helix chain 'A' and resid 261 through 265 removed outlier: 3.809A pdb=" N PHE A 264 " --> pdb=" O CYS A 261 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 278 Processing helix chain 'A' and resid 307 through 319 Processing helix chain 'A' and resid 382 through 386 removed outlier: 4.337A pdb=" N PHE A 386 " --> pdb=" O TRP A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 408 through 433 Processing helix chain 'A' and resid 433 through 455 removed outlier: 6.712A pdb=" N LEU A 446 " --> pdb=" O GLU A 442 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N PHE A 447 " --> pdb=" O ASP A 443 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N MET A 448 " --> pdb=" O TYR A 444 " (cutoff:3.500A) Processing helix chain 'A' and resid 457 through 466 Processing helix chain 'A' and resid 482 through 490 removed outlier: 3.579A pdb=" N ARG A 489 " --> pdb=" O GLU A 485 " (cutoff:3.500A) Processing helix chain 'A' and resid 504 through 510 Processing helix chain 'A' and resid 511 through 518 Processing helix chain 'A' and resid 531 through 540 Processing helix chain 'A' and resid 550 through 557 Processing helix chain 'A' and resid 575 through 590 Processing helix chain 'A' and resid 614 through 628 Processing helix chain 'A' and resid 648 through 658 removed outlier: 3.743A pdb=" N LEU A 654 " --> pdb=" O LEU A 650 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N ASN A 655 " --> pdb=" O ILE A 651 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N GLN A 656 " --> pdb=" O LYS A 652 " (cutoff:3.500A) Processing helix chain 'A' and resid 661 through 680 Processing helix chain 'A' and resid 686 through 700 removed outlier: 3.758A pdb=" N VAL A 690 " --> pdb=" O PRO A 686 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N GLY A 691 " --> pdb=" O ARG A 687 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ARG A 692 " --> pdb=" O ALA A 688 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 104 Processing helix chain 'B' and resid 110 through 134 removed outlier: 4.129A pdb=" N ARG B 114 " --> pdb=" O GLU B 110 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ASP B 134 " --> pdb=" O LYS B 130 " (cutoff:3.500A) Processing helix chain 'B' and resid 164 through 172 Processing helix chain 'B' and resid 178 through 186 removed outlier: 4.032A pdb=" N ALA B 182 " --> pdb=" O SER B 178 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 210 Processing helix chain 'B' and resid 261 through 265 Processing helix chain 'B' and resid 266 through 278 Processing helix chain 'B' and resid 302 through 306 removed outlier: 3.520A pdb=" N VAL B 306 " --> pdb=" O PRO B 303 " (cutoff:3.500A) Processing helix chain 'B' and resid 307 through 320 Processing helix chain 'B' and resid 381 through 387 removed outlier: 4.344A pdb=" N PHE B 386 " --> pdb=" O TRP B 383 " (cutoff:3.500A) Processing helix chain 'B' and resid 408 through 433 Processing helix chain 'B' and resid 434 through 455 removed outlier: 6.858A pdb=" N LEU B 446 " --> pdb=" O GLU B 442 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N PHE B 447 " --> pdb=" O ASP B 443 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N MET B 448 " --> pdb=" O TYR B 444 " (cutoff:3.500A) Processing helix chain 'B' and resid 457 through 466 Processing helix chain 'B' and resid 483 through 490 Processing helix chain 'B' and resid 504 through 510 Processing helix chain 'B' and resid 511 through 518 Processing helix chain 'B' and resid 532 through 540 Processing helix chain 'B' and resid 550 through 557 Processing helix chain 'B' and resid 575 through 590 Processing helix chain 'B' and resid 614 through 623 removed outlier: 3.584A pdb=" N HIS B 620 " --> pdb=" O GLY B 616 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ARG B 623 " --> pdb=" O ARG B 619 " (cutoff:3.500A) Processing helix chain 'B' and resid 631 through 639 Processing helix chain 'B' and resid 648 through 661 removed outlier: 3.721A pdb=" N GLN B 656 " --> pdb=" O LYS B 652 " (cutoff:3.500A) removed outlier: 4.990A pdb=" N ALA B 659 " --> pdb=" O ASN B 655 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N SER B 660 " --> pdb=" O GLN B 656 " (cutoff:3.500A) Processing helix chain 'B' and resid 661 through 680 Processing helix chain 'B' and resid 688 through 701 removed outlier: 4.488A pdb=" N ARG B 692 " --> pdb=" O ALA B 688 " (cutoff:3.500A) Processing helix chain 'B' and resid 702 through 704 No H-bonds generated for 'chain 'B' and resid 702 through 704' Processing helix chain 'C' and resid 66 through 68 No H-bonds generated for 'chain 'C' and resid 66 through 68' Processing helix chain 'C' and resid 71 through 82 removed outlier: 3.857A pdb=" N ALA C 75 " --> pdb=" O MET C 71 " (cutoff:3.500A) Processing helix chain 'C' and resid 135 through 140 removed outlier: 4.418A pdb=" N VAL C 140 " --> pdb=" O ILE C 136 " (cutoff:3.500A) Processing helix chain 'C' and resid 145 through 152 removed outlier: 3.791A pdb=" N GLN C 149 " --> pdb=" O ASN C 145 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 80 through 81 Processing sheet with id=AA2, first strand: chain 'A' and resid 80 through 81 removed outlier: 4.005A pdb=" N ARG B 214 " --> pdb=" O HIS B 256 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 91 through 92 removed outlier: 7.228A pdb=" N GLN A 91 " --> pdb=" O ILE B 175 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 290 through 291 removed outlier: 4.233A pdb=" N ARG A 214 " --> pdb=" O HIS A 256 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 290 through 291 removed outlier: 4.233A pdb=" N ARG A 214 " --> pdb=" O HIS A 256 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 174 through 175 Processing sheet with id=AA7, first strand: chain 'A' and resid 325 through 333 removed outlier: 3.840A pdb=" N TYR A 327 " --> pdb=" O VAL A 345 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 471 through 472 removed outlier: 3.706A pdb=" N GLU A 471 " --> pdb=" O PHE A 526 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N TYR A 499 " --> pdb=" O ILE A 548 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 596 through 599 removed outlier: 6.290A pdb=" N ASN A 596 " --> pdb=" O LEU A 642 " (cutoff:3.500A) removed outlier: 7.829A pdb=" N ILE A 644 " --> pdb=" O ASN A 596 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N LYS A 598 " --> pdb=" O ILE A 644 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 325 through 333 removed outlier: 3.589A pdb=" N TYR B 327 " --> pdb=" O VAL B 345 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N SER B 393 " --> pdb=" O TYR B 366 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 469 through 470 Processing sheet with id=AB3, first strand: chain 'B' and resid 524 through 527 removed outlier: 8.950A pdb=" N LEU B 525 " --> pdb=" O ASN B 496 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N TYR B 498 " --> pdb=" O LEU B 525 " (cutoff:3.500A) removed outlier: 7.922A pdb=" N CYS B 527 " --> pdb=" O TYR B 498 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N LEU B 500 " --> pdb=" O CYS B 527 " (cutoff:3.500A) removed outlier: 5.515A pdb=" N ILE B 497 " --> pdb=" O ILE B 548 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'B' and resid 597 through 599 removed outlier: 6.518A pdb=" N LYS B 598 " --> pdb=" O ILE B 644 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N THR B 641 " --> pdb=" O THR B 611 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 57 through 64 removed outlier: 4.306A pdb=" N HIS C 57 " --> pdb=" O ARG C 46 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N ARG C 46 " --> pdb=" O HIS C 57 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N GLN C 59 " --> pdb=" O ILE C 44 " (cutoff:3.500A) removed outlier: 9.195A pdb=" N SER C 125 " --> pdb=" O ILE C 39 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N LYS C 41 " --> pdb=" O SER C 125 " (cutoff:3.500A) removed outlier: 7.338A pdb=" N ILE C 127 " --> pdb=" O LYS C 41 " (cutoff:3.500A) removed outlier: 5.900A pdb=" N ALA C 43 " --> pdb=" O ILE C 127 " (cutoff:3.500A) 537 hydrogen bonds defined for protein. 1488 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.54 Time building geometry restraints manager: 1.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.42: 4537 1.42 - 1.62: 6393 1.62 - 1.81: 96 1.81 - 2.01: 1 2.01 - 2.20: 4 Bond restraints: 11031 Sorted by residual: bond pdb=" O3A ANP A 801 " pdb=" PB ANP A 801 " ideal model delta sigma weight residual 1.700 1.556 0.144 2.00e-02 2.50e+03 5.17e+01 bond pdb=" O3A ANP B 801 " pdb=" PB ANP B 801 " ideal model delta sigma weight residual 1.700 1.557 0.143 2.00e-02 2.50e+03 5.11e+01 bond pdb=" N3B ANP A 801 " pdb=" PG ANP A 801 " ideal model delta sigma weight residual 1.795 1.691 0.104 2.00e-02 2.50e+03 2.73e+01 bond pdb=" N3B ANP B 801 " pdb=" PG ANP B 801 " ideal model delta sigma weight residual 1.795 1.691 0.104 2.00e-02 2.50e+03 2.71e+01 bond pdb=" O5' ANP A 801 " pdb=" PA ANP A 801 " ideal model delta sigma weight residual 1.655 1.579 0.076 2.00e-02 2.50e+03 1.44e+01 ... (remaining 11026 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.37: 14812 3.37 - 6.73: 61 6.73 - 10.10: 9 10.10 - 13.46: 2 13.46 - 16.83: 2 Bond angle restraints: 14886 Sorted by residual: angle pdb=" PB ANP A 801 " pdb=" N3B ANP A 801 " pdb=" PG ANP A 801 " ideal model delta sigma weight residual 126.95 110.12 16.83 3.00e+00 1.11e-01 3.15e+01 angle pdb=" PB ANP B 801 " pdb=" N3B ANP B 801 " pdb=" PG ANP B 801 " ideal model delta sigma weight residual 126.95 110.27 16.68 3.00e+00 1.11e-01 3.09e+01 angle pdb=" O1B ANP B 801 " pdb=" PB ANP B 801 " pdb=" O2B ANP B 801 " ideal model delta sigma weight residual 120.08 108.91 11.17 3.00e+00 1.11e-01 1.39e+01 angle pdb=" O1B ANP A 801 " pdb=" PB ANP A 801 " pdb=" O2B ANP A 801 " ideal model delta sigma weight residual 120.08 108.95 11.13 3.00e+00 1.11e-01 1.38e+01 angle pdb=" CA ARG C 94 " pdb=" CB ARG C 94 " pdb=" CG ARG C 94 " ideal model delta sigma weight residual 114.10 120.88 -6.78 2.00e+00 2.50e-01 1.15e+01 ... (remaining 14881 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.88: 6005 17.88 - 35.75: 612 35.75 - 53.62: 126 53.62 - 71.50: 35 71.50 - 89.37: 16 Dihedral angle restraints: 6794 sinusoidal: 2839 harmonic: 3955 Sorted by residual: dihedral pdb=" CA LEU C 130 " pdb=" C LEU C 130 " pdb=" N PRO C 131 " pdb=" CA PRO C 131 " ideal model delta harmonic sigma weight residual -180.00 -156.16 -23.84 0 5.00e+00 4.00e-02 2.27e+01 dihedral pdb=" CA TYR B 277 " pdb=" C TYR B 277 " pdb=" N SER B 278 " pdb=" CA SER B 278 " ideal model delta harmonic sigma weight residual -180.00 -162.36 -17.64 0 5.00e+00 4.00e-02 1.25e+01 dihedral pdb=" CA ASP B 158 " pdb=" CB ASP B 158 " pdb=" CG ASP B 158 " pdb=" OD1 ASP B 158 " ideal model delta sinusoidal sigma weight residual -30.00 -88.78 58.78 1 2.00e+01 2.50e-03 1.16e+01 ... (remaining 6791 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 1432 0.055 - 0.109: 207 0.109 - 0.164: 32 0.164 - 0.219: 1 0.219 - 0.273: 2 Chirality restraints: 1674 Sorted by residual: chirality pdb=" C3' ANP B 801 " pdb=" C2' ANP B 801 " pdb=" C4' ANP B 801 " pdb=" O3' ANP B 801 " both_signs ideal model delta sigma weight residual False -2.36 -2.63 0.27 2.00e-01 2.50e+01 1.87e+00 chirality pdb=" C3' ANP A 801 " pdb=" C2' ANP A 801 " pdb=" C4' ANP A 801 " pdb=" O3' ANP A 801 " both_signs ideal model delta sigma weight residual False -2.36 -2.63 0.27 2.00e-01 2.50e+01 1.85e+00 chirality pdb=" CA GLU C 154 " pdb=" N GLU C 154 " pdb=" C GLU C 154 " pdb=" CB GLU C 154 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.81e-01 ... (remaining 1671 not shown) Planarity restraints: 1889 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU A 661 " 0.068 5.00e-02 4.00e+02 1.03e-01 1.69e+01 pdb=" N PRO A 662 " -0.178 5.00e-02 4.00e+02 pdb=" CA PRO A 662 " 0.053 5.00e-02 4.00e+02 pdb=" CD PRO A 662 " 0.056 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 585 " -0.012 2.00e-02 2.50e+03 1.20e-02 3.62e+00 pdb=" CG TRP B 585 " 0.033 2.00e-02 2.50e+03 pdb=" CD1 TRP B 585 " -0.015 2.00e-02 2.50e+03 pdb=" CD2 TRP B 585 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP B 585 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP B 585 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP B 585 " -0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 585 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 585 " -0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP B 585 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 585 " 0.011 2.00e-02 2.50e+03 9.12e-03 2.08e+00 pdb=" CG TRP A 585 " -0.025 2.00e-02 2.50e+03 pdb=" CD1 TRP A 585 " 0.010 2.00e-02 2.50e+03 pdb=" CD2 TRP A 585 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP A 585 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP A 585 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A 585 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 585 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 585 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP A 585 " 0.002 2.00e-02 2.50e+03 ... (remaining 1886 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.62: 148 2.62 - 3.25: 10854 3.25 - 3.88: 22134 3.88 - 4.51: 29363 4.51 - 5.14: 46205 Nonbonded interactions: 108704 Sorted by model distance: nonbonded pdb=" O3G ANP A 801 " pdb="MG MG A 802 " model vdw 1.994 2.170 nonbonded pdb=" OD1 ASN A 119 " pdb="MG MG A 802 " model vdw 2.010 2.170 nonbonded pdb=" O3G ANP B 801 " pdb="MG MG B 802 " model vdw 2.042 2.170 nonbonded pdb=" OD1 ASN B 119 " pdb="MG MG B 802 " model vdw 2.048 2.170 nonbonded pdb=" O1B ANP B 801 " pdb="MG MG B 802 " model vdw 2.068 2.170 ... (remaining 108699 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 70 through 355 or resid 361 through 626 or resid 631 throu \ gh 803)) selection = (chain 'B' and (resid 70 through 355 or resid 361 through 625 or resid 631 or re \ sid 636 through 803)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.230 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.000 Extract box with map and model: 0.220 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.320 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.144 11035 Z= 0.188 Angle : 0.650 16.828 14892 Z= 0.322 Chirality : 0.041 0.273 1674 Planarity : 0.003 0.103 1889 Dihedral : 15.796 89.374 4226 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 0.00 % Allowed : 0.17 % Favored : 99.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.75 (0.25), residues: 1329 helix: 1.26 (0.24), residues: 543 sheet: 1.47 (0.40), residues: 200 loop : -0.55 (0.28), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 540 TYR 0.014 0.001 TYR C 150 PHE 0.012 0.001 PHE A 112 TRP 0.033 0.002 TRP B 585 HIS 0.007 0.001 HIS A 311 Details of bonding type rmsd covalent geometry : bond 0.00381 (11031) covalent geometry : angle 0.64298 (14886) hydrogen bonds : bond 0.16567 ( 502) hydrogen bonds : angle 6.53142 ( 1488) metal coordination : bond 0.00579 ( 4) metal coordination : angle 4.84622 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2658 Ramachandran restraints generated. 1329 Oldfield, 0 Emsley, 1329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2658 Ramachandran restraints generated. 1329 Oldfield, 0 Emsley, 1329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 141 time to evaluate : 0.480 Fit side-chains revert: symmetry clash REVERT: A 586 MET cc_start: 0.8787 (mpp) cc_final: 0.7777 (mpp) REVERT: B 292 MET cc_start: 0.7199 (ppp) cc_final: 0.6933 (ppp) REVERT: B 517 MET cc_start: 0.6882 (tmm) cc_final: 0.6580 (tmm) REVERT: B 576 GLU cc_start: 0.7480 (tp30) cc_final: 0.7231 (tp30) REVERT: C 44 ILE cc_start: 0.8049 (mt) cc_final: 0.7838 (mm) outliers start: 0 outliers final: 0 residues processed: 141 average time/residue: 0.0929 time to fit residues: 19.3309 Evaluate side-chains 112 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 112 time to evaluate : 0.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 98 optimal weight: 5.9990 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 0.0670 chunk 124 optimal weight: 20.0000 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 8.9990 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 4.9990 chunk 55 optimal weight: 5.9990 overall best weight: 1.3720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 506 HIS A 620 HIS A 704 HIS B 288 ASN B 510 HIS B 671 GLN C 132 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.116646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.092517 restraints weight = 20884.668| |-----------------------------------------------------------------------------| r_work (start): 0.3270 rms_B_bonded: 2.92 r_work: 0.3068 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 moved from start: 0.1149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11035 Z= 0.153 Angle : 0.570 11.232 14892 Z= 0.285 Chirality : 0.042 0.163 1674 Planarity : 0.004 0.071 1889 Dihedral : 5.555 59.565 1540 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 0.51 % Allowed : 9.25 % Favored : 90.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.66 (0.24), residues: 1329 helix: 1.24 (0.23), residues: 538 sheet: 1.08 (0.39), residues: 200 loop : -0.49 (0.28), residues: 591 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 495 TYR 0.014 0.001 TYR B 218 PHE 0.019 0.001 PHE C 146 TRP 0.015 0.002 TRP B 585 HIS 0.010 0.001 HIS B 620 Details of bonding type rmsd covalent geometry : bond 0.00346 (11031) covalent geometry : angle 0.55261 (14886) hydrogen bonds : bond 0.03606 ( 502) hydrogen bonds : angle 4.88561 ( 1488) metal coordination : bond 0.01200 ( 4) metal coordination : angle 6.94251 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2658 Ramachandran restraints generated. 1329 Oldfield, 0 Emsley, 1329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2658 Ramachandran restraints generated. 1329 Oldfield, 0 Emsley, 1329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 118 time to evaluate : 0.409 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 583 MET cc_start: 0.7706 (mtm) cc_final: 0.7456 (mtm) REVERT: B 517 MET cc_start: 0.7645 (tmm) cc_final: 0.7273 (tmm) outliers start: 6 outliers final: 3 residues processed: 120 average time/residue: 0.1015 time to fit residues: 17.5897 Evaluate side-chains 114 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 111 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 622 LEU Chi-restraints excluded: chain B residue 379 ILE Chi-restraints excluded: chain B residue 390 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 89 optimal weight: 9.9990 chunk 67 optimal weight: 4.9990 chunk 109 optimal weight: 9.9990 chunk 114 optimal weight: 6.9990 chunk 104 optimal weight: 0.9980 chunk 106 optimal weight: 2.9990 chunk 64 optimal weight: 3.9990 chunk 26 optimal weight: 0.9980 chunk 38 optimal weight: 2.9990 chunk 107 optimal weight: 0.7980 chunk 4 optimal weight: 0.8980 overall best weight: 1.3382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 510 HIS B 620 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.114700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.090282 restraints weight = 21094.345| |-----------------------------------------------------------------------------| r_work (start): 0.3245 rms_B_bonded: 2.84 r_work: 0.3034 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 moved from start: 0.1459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11035 Z= 0.147 Angle : 0.544 13.173 14892 Z= 0.272 Chirality : 0.041 0.157 1674 Planarity : 0.003 0.060 1889 Dihedral : 5.343 53.557 1540 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 0.85 % Allowed : 11.38 % Favored : 87.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.57 (0.24), residues: 1329 helix: 1.26 (0.23), residues: 538 sheet: 0.86 (0.39), residues: 193 loop : -0.55 (0.27), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 495 TYR 0.013 0.001 TYR A 437 PHE 0.008 0.001 PHE B 264 TRP 0.019 0.002 TRP B 585 HIS 0.005 0.001 HIS B 620 Details of bonding type rmsd covalent geometry : bond 0.00335 (11031) covalent geometry : angle 0.52778 (14886) hydrogen bonds : bond 0.03375 ( 502) hydrogen bonds : angle 4.67213 ( 1488) metal coordination : bond 0.00899 ( 4) metal coordination : angle 6.52228 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2658 Ramachandran restraints generated. 1329 Oldfield, 0 Emsley, 1329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2658 Ramachandran restraints generated. 1329 Oldfield, 0 Emsley, 1329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 124 time to evaluate : 0.400 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 586 MET cc_start: 0.8981 (mpp) cc_final: 0.8403 (mpp) REVERT: B 292 MET cc_start: 0.8132 (ppp) cc_final: 0.7740 (ppp) REVERT: B 517 MET cc_start: 0.7755 (tmm) cc_final: 0.7394 (tmm) REVERT: B 576 GLU cc_start: 0.7767 (tp30) cc_final: 0.7489 (tp30) REVERT: B 692 ARG cc_start: 0.8531 (mtm180) cc_final: 0.8299 (mtt90) REVERT: C 44 ILE cc_start: 0.8223 (mm) cc_final: 0.8016 (mp) outliers start: 10 outliers final: 5 residues processed: 129 average time/residue: 0.1022 time to fit residues: 19.2232 Evaluate side-chains 120 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 115 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 622 LEU Chi-restraints excluded: chain A residue 690 VAL Chi-restraints excluded: chain B residue 390 VAL Chi-restraints excluded: chain C residue 146 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 99 optimal weight: 1.9990 chunk 1 optimal weight: 10.0000 chunk 26 optimal weight: 0.9980 chunk 88 optimal weight: 0.9990 chunk 52 optimal weight: 3.9990 chunk 97 optimal weight: 5.9990 chunk 40 optimal weight: 0.8980 chunk 48 optimal weight: 7.9990 chunk 68 optimal weight: 6.9990 chunk 70 optimal weight: 4.9990 chunk 42 optimal weight: 3.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.112819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.087964 restraints weight = 21060.470| |-----------------------------------------------------------------------------| r_work (start): 0.3216 rms_B_bonded: 2.88 r_work: 0.3014 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8536 moved from start: 0.1821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 11035 Z= 0.177 Angle : 0.567 14.075 14892 Z= 0.280 Chirality : 0.042 0.162 1674 Planarity : 0.003 0.053 1889 Dihedral : 5.376 51.513 1540 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 1.70 % Allowed : 13.24 % Favored : 85.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.51 (0.24), residues: 1329 helix: 1.22 (0.23), residues: 539 sheet: 0.82 (0.38), residues: 190 loop : -0.59 (0.27), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 495 TYR 0.018 0.002 TYR A 315 PHE 0.010 0.001 PHE B 264 TRP 0.022 0.002 TRP A 585 HIS 0.004 0.001 HIS A 330 Details of bonding type rmsd covalent geometry : bond 0.00404 (11031) covalent geometry : angle 0.55263 (14886) hydrogen bonds : bond 0.03329 ( 502) hydrogen bonds : angle 4.63123 ( 1488) metal coordination : bond 0.01290 ( 4) metal coordination : angle 6.44751 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2658 Ramachandran restraints generated. 1329 Oldfield, 0 Emsley, 1329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2658 Ramachandran restraints generated. 1329 Oldfield, 0 Emsley, 1329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 117 time to evaluate : 0.450 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 462 GLU cc_start: 0.8096 (OUTLIER) cc_final: 0.7620 (mp0) REVERT: A 586 MET cc_start: 0.9018 (OUTLIER) cc_final: 0.8513 (mpp) REVERT: B 292 MET cc_start: 0.8221 (ppp) cc_final: 0.7661 (ppp) REVERT: B 576 GLU cc_start: 0.7810 (tp30) cc_final: 0.7529 (tp30) REVERT: B 692 ARG cc_start: 0.8566 (mtm180) cc_final: 0.8118 (mtt90) outliers start: 20 outliers final: 10 residues processed: 130 average time/residue: 0.0925 time to fit residues: 17.6025 Evaluate side-chains 122 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 110 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 462 GLU Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 586 MET Chi-restraints excluded: chain A residue 622 LEU Chi-restraints excluded: chain A residue 690 VAL Chi-restraints excluded: chain B residue 306 VAL Chi-restraints excluded: chain B residue 390 VAL Chi-restraints excluded: chain B residue 672 ILE Chi-restraints excluded: chain B residue 683 VAL Chi-restraints excluded: chain C residue 146 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 7 optimal weight: 5.9990 chunk 97 optimal weight: 1.9990 chunk 118 optimal weight: 0.9990 chunk 49 optimal weight: 6.9990 chunk 91 optimal weight: 4.9990 chunk 101 optimal weight: 3.9990 chunk 38 optimal weight: 0.9990 chunk 67 optimal weight: 6.9990 chunk 116 optimal weight: 7.9990 chunk 16 optimal weight: 7.9990 chunk 60 optimal weight: 0.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 190 GLN B 279 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.112686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.088229 restraints weight = 21002.602| |-----------------------------------------------------------------------------| r_work (start): 0.3200 rms_B_bonded: 2.79 r_work: 0.2991 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8553 moved from start: 0.2024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 11035 Z= 0.176 Angle : 0.564 14.019 14892 Z= 0.279 Chirality : 0.042 0.163 1674 Planarity : 0.003 0.050 1889 Dihedral : 5.367 50.528 1540 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 2.04 % Allowed : 14.77 % Favored : 83.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.41 (0.24), residues: 1329 helix: 1.17 (0.23), residues: 540 sheet: 0.69 (0.38), residues: 191 loop : -0.67 (0.26), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 469 TYR 0.017 0.002 TYR A 315 PHE 0.012 0.001 PHE C 146 TRP 0.025 0.002 TRP A 585 HIS 0.004 0.001 HIS A 330 Details of bonding type rmsd covalent geometry : bond 0.00404 (11031) covalent geometry : angle 0.54656 (14886) hydrogen bonds : bond 0.03282 ( 502) hydrogen bonds : angle 4.62979 ( 1488) metal coordination : bond 0.01295 ( 4) metal coordination : angle 6.91179 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2658 Ramachandran restraints generated. 1329 Oldfield, 0 Emsley, 1329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2658 Ramachandran restraints generated. 1329 Oldfield, 0 Emsley, 1329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 123 time to evaluate : 0.386 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 462 GLU cc_start: 0.8073 (OUTLIER) cc_final: 0.7555 (mp0) REVERT: A 586 MET cc_start: 0.9008 (OUTLIER) cc_final: 0.8419 (mpp) REVERT: A 609 MET cc_start: 0.8732 (ttm) cc_final: 0.8517 (ttp) REVERT: B 98 LEU cc_start: 0.9397 (OUTLIER) cc_final: 0.9004 (mm) REVERT: B 517 MET cc_start: 0.7865 (tmm) cc_final: 0.7659 (tmm) REVERT: B 576 GLU cc_start: 0.7811 (tp30) cc_final: 0.7517 (tp30) REVERT: B 692 ARG cc_start: 0.8598 (mtm180) cc_final: 0.8292 (mtt90) REVERT: C 151 LYS cc_start: 0.8651 (mmtp) cc_final: 0.8424 (mmtt) outliers start: 24 outliers final: 13 residues processed: 139 average time/residue: 0.0946 time to fit residues: 19.3020 Evaluate side-chains 127 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 111 time to evaluate : 0.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 210 MET Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 442 GLU Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain A residue 462 GLU Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 586 MET Chi-restraints excluded: chain A residue 622 LEU Chi-restraints excluded: chain A residue 690 VAL Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 306 VAL Chi-restraints excluded: chain B residue 390 VAL Chi-restraints excluded: chain B residue 672 ILE Chi-restraints excluded: chain B residue 683 VAL Chi-restraints excluded: chain C residue 146 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 80 optimal weight: 0.0970 chunk 15 optimal weight: 10.0000 chunk 85 optimal weight: 0.8980 chunk 17 optimal weight: 2.9990 chunk 4 optimal weight: 0.8980 chunk 8 optimal weight: 3.9990 chunk 72 optimal weight: 0.9990 chunk 7 optimal weight: 0.8980 chunk 32 optimal weight: 0.9990 chunk 28 optimal weight: 10.0000 chunk 10 optimal weight: 4.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 279 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.114895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.089968 restraints weight = 21096.376| |-----------------------------------------------------------------------------| r_work (start): 0.3229 rms_B_bonded: 3.00 r_work: 0.3028 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8516 moved from start: 0.2049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 11035 Z= 0.111 Angle : 0.532 13.342 14892 Z= 0.262 Chirality : 0.041 0.166 1674 Planarity : 0.003 0.050 1889 Dihedral : 5.117 45.802 1540 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 2.21 % Allowed : 14.69 % Favored : 83.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.49 (0.24), residues: 1329 helix: 1.27 (0.23), residues: 539 sheet: 0.57 (0.38), residues: 193 loop : -0.59 (0.27), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 128 TYR 0.013 0.001 TYR A 315 PHE 0.010 0.001 PHE C 146 TRP 0.028 0.002 TRP A 585 HIS 0.004 0.001 HIS A 311 Details of bonding type rmsd covalent geometry : bond 0.00250 (11031) covalent geometry : angle 0.51770 (14886) hydrogen bonds : bond 0.03017 ( 502) hydrogen bonds : angle 4.47474 ( 1488) metal coordination : bond 0.00778 ( 4) metal coordination : angle 6.14077 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2658 Ramachandran restraints generated. 1329 Oldfield, 0 Emsley, 1329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2658 Ramachandran restraints generated. 1329 Oldfield, 0 Emsley, 1329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 122 time to evaluate : 0.369 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 462 GLU cc_start: 0.8086 (OUTLIER) cc_final: 0.7512 (mp0) REVERT: A 586 MET cc_start: 0.8933 (OUTLIER) cc_final: 0.8368 (mpp) REVERT: A 609 MET cc_start: 0.8657 (ttm) cc_final: 0.8417 (ttp) REVERT: B 98 LEU cc_start: 0.9395 (OUTLIER) cc_final: 0.9024 (mm) REVERT: B 292 MET cc_start: 0.8087 (ppp) cc_final: 0.7627 (ppp) REVERT: B 576 GLU cc_start: 0.7798 (tp30) cc_final: 0.7501 (tp30) REVERT: B 586 MET cc_start: 0.8730 (mtm) cc_final: 0.8428 (mtt) REVERT: B 670 ASP cc_start: 0.8703 (t70) cc_final: 0.8485 (m-30) REVERT: C 151 LYS cc_start: 0.8634 (mmtp) cc_final: 0.8395 (mmtt) outliers start: 26 outliers final: 12 residues processed: 138 average time/residue: 0.0915 time to fit residues: 18.6216 Evaluate side-chains 127 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 112 time to evaluate : 0.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 MET Chi-restraints excluded: chain A residue 442 GLU Chi-restraints excluded: chain A residue 462 GLU Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 586 MET Chi-restraints excluded: chain A residue 622 LEU Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 110 GLU Chi-restraints excluded: chain B residue 306 VAL Chi-restraints excluded: chain B residue 390 VAL Chi-restraints excluded: chain B residue 537 LEU Chi-restraints excluded: chain B residue 683 VAL Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 146 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 90 optimal weight: 2.9990 chunk 92 optimal weight: 0.8980 chunk 119 optimal weight: 0.9990 chunk 123 optimal weight: 0.2980 chunk 127 optimal weight: 9.9990 chunk 132 optimal weight: 9.9990 chunk 11 optimal weight: 0.9980 chunk 57 optimal weight: 0.9990 chunk 80 optimal weight: 0.9980 chunk 96 optimal weight: 0.9990 chunk 76 optimal weight: 8.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 279 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.116842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.093698 restraints weight = 20987.646| |-----------------------------------------------------------------------------| r_work (start): 0.3331 rms_B_bonded: 2.63 r_work: 0.3132 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8486 moved from start: 0.2085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11035 Z= 0.114 Angle : 0.548 13.852 14892 Z= 0.268 Chirality : 0.041 0.179 1674 Planarity : 0.003 0.047 1889 Dihedral : 5.042 43.702 1540 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 2.21 % Allowed : 15.37 % Favored : 82.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.48 (0.24), residues: 1329 helix: 1.27 (0.23), residues: 540 sheet: 0.57 (0.38), residues: 193 loop : -0.60 (0.27), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 692 TYR 0.015 0.001 TYR A 315 PHE 0.010 0.001 PHE C 146 TRP 0.029 0.002 TRP A 585 HIS 0.004 0.001 HIS B 620 Details of bonding type rmsd covalent geometry : bond 0.00261 (11031) covalent geometry : angle 0.53339 (14886) hydrogen bonds : bond 0.02969 ( 502) hydrogen bonds : angle 4.43980 ( 1488) metal coordination : bond 0.01017 ( 4) metal coordination : angle 6.19915 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2658 Ramachandran restraints generated. 1329 Oldfield, 0 Emsley, 1329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2658 Ramachandran restraints generated. 1329 Oldfield, 0 Emsley, 1329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 117 time to evaluate : 0.411 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 462 GLU cc_start: 0.7959 (OUTLIER) cc_final: 0.7383 (mp0) REVERT: A 586 MET cc_start: 0.8937 (OUTLIER) cc_final: 0.8385 (mpp) REVERT: A 609 MET cc_start: 0.8641 (ttm) cc_final: 0.8418 (ttp) REVERT: B 98 LEU cc_start: 0.9384 (OUTLIER) cc_final: 0.9037 (mm) REVERT: B 292 MET cc_start: 0.7945 (ppp) cc_final: 0.7528 (ppp) REVERT: B 586 MET cc_start: 0.8752 (mtm) cc_final: 0.8452 (mtt) REVERT: B 692 ARG cc_start: 0.8488 (mtt90) cc_final: 0.8218 (mtt90) outliers start: 26 outliers final: 19 residues processed: 136 average time/residue: 0.0932 time to fit residues: 18.7049 Evaluate side-chains 136 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 114 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 ILE Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 210 MET Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 442 GLU Chi-restraints excluded: chain A residue 462 GLU Chi-restraints excluded: chain A residue 480 LEU Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 586 MET Chi-restraints excluded: chain A residue 599 VAL Chi-restraints excluded: chain A residue 622 LEU Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 110 GLU Chi-restraints excluded: chain B residue 279 ASN Chi-restraints excluded: chain B residue 306 VAL Chi-restraints excluded: chain B residue 379 ILE Chi-restraints excluded: chain B residue 390 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 537 LEU Chi-restraints excluded: chain B residue 683 VAL Chi-restraints excluded: chain C residue 146 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 60 optimal weight: 4.9990 chunk 30 optimal weight: 0.4980 chunk 23 optimal weight: 0.9990 chunk 94 optimal weight: 4.9990 chunk 108 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 47 optimal weight: 4.9990 chunk 42 optimal weight: 3.9990 chunk 75 optimal weight: 5.9990 chunk 95 optimal weight: 1.9990 chunk 100 optimal weight: 0.9990 overall best weight: 1.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 279 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.114403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.089327 restraints weight = 21140.683| |-----------------------------------------------------------------------------| r_work (start): 0.3216 rms_B_bonded: 2.96 r_work: 0.3005 rms_B_bonded: 4.16 restraints_weight: 0.5000 r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8540 moved from start: 0.2177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11035 Z= 0.141 Angle : 0.560 13.932 14892 Z= 0.275 Chirality : 0.041 0.187 1674 Planarity : 0.003 0.050 1889 Dihedral : 5.084 44.387 1540 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 2.29 % Allowed : 15.53 % Favored : 82.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.46 (0.24), residues: 1329 helix: 1.26 (0.23), residues: 539 sheet: 0.54 (0.38), residues: 193 loop : -0.62 (0.27), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 290 TYR 0.023 0.002 TYR C 147 PHE 0.011 0.001 PHE C 146 TRP 0.030 0.002 TRP A 585 HIS 0.005 0.001 HIS B 620 Details of bonding type rmsd covalent geometry : bond 0.00325 (11031) covalent geometry : angle 0.54586 (14886) hydrogen bonds : bond 0.03004 ( 502) hydrogen bonds : angle 4.45771 ( 1488) metal coordination : bond 0.01147 ( 4) metal coordination : angle 6.25980 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2658 Ramachandran restraints generated. 1329 Oldfield, 0 Emsley, 1329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2658 Ramachandran restraints generated. 1329 Oldfield, 0 Emsley, 1329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 114 time to evaluate : 0.406 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 462 GLU cc_start: 0.8080 (OUTLIER) cc_final: 0.7500 (mp0) REVERT: A 586 MET cc_start: 0.8955 (OUTLIER) cc_final: 0.8403 (mpp) REVERT: B 98 LEU cc_start: 0.9403 (OUTLIER) cc_final: 0.9042 (mm) REVERT: B 292 MET cc_start: 0.8123 (ppp) cc_final: 0.7660 (ppp) REVERT: B 586 MET cc_start: 0.8717 (mtm) cc_final: 0.8413 (mtt) outliers start: 27 outliers final: 21 residues processed: 134 average time/residue: 0.0891 time to fit residues: 17.7183 Evaluate side-chains 136 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 112 time to evaluate : 0.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 ILE Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 210 MET Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 442 GLU Chi-restraints excluded: chain A residue 462 GLU Chi-restraints excluded: chain A residue 480 LEU Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 527 CYS Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 586 MET Chi-restraints excluded: chain A residue 599 VAL Chi-restraints excluded: chain A residue 622 LEU Chi-restraints excluded: chain B residue 72 HIS Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 110 GLU Chi-restraints excluded: chain B residue 306 VAL Chi-restraints excluded: chain B residue 379 ILE Chi-restraints excluded: chain B residue 390 VAL Chi-restraints excluded: chain B residue 446 LEU Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 537 LEU Chi-restraints excluded: chain B residue 683 VAL Chi-restraints excluded: chain C residue 146 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 34 optimal weight: 3.9990 chunk 121 optimal weight: 2.9990 chunk 127 optimal weight: 4.9990 chunk 97 optimal weight: 1.9990 chunk 9 optimal weight: 5.9990 chunk 132 optimal weight: 3.9990 chunk 73 optimal weight: 0.5980 chunk 14 optimal weight: 0.9980 chunk 45 optimal weight: 0.0770 chunk 131 optimal weight: 9.9990 chunk 72 optimal weight: 4.9990 overall best weight: 1.3342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 279 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.114030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.089398 restraints weight = 21009.717| |-----------------------------------------------------------------------------| r_work (start): 0.3218 rms_B_bonded: 2.85 r_work: 0.3010 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8538 moved from start: 0.2258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11035 Z= 0.145 Angle : 0.570 14.126 14892 Z= 0.280 Chirality : 0.041 0.188 1674 Planarity : 0.003 0.051 1889 Dihedral : 5.123 44.709 1540 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 2.29 % Allowed : 15.87 % Favored : 81.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.44 (0.24), residues: 1329 helix: 1.22 (0.23), residues: 539 sheet: 0.54 (0.39), residues: 194 loop : -0.62 (0.27), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 290 TYR 0.043 0.002 TYR C 147 PHE 0.012 0.001 PHE C 146 TRP 0.032 0.002 TRP A 585 HIS 0.005 0.001 HIS B 620 Details of bonding type rmsd covalent geometry : bond 0.00336 (11031) covalent geometry : angle 0.55600 (14886) hydrogen bonds : bond 0.03047 ( 502) hydrogen bonds : angle 4.48769 ( 1488) metal coordination : bond 0.01262 ( 4) metal coordination : angle 6.30853 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2658 Ramachandran restraints generated. 1329 Oldfield, 0 Emsley, 1329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2658 Ramachandran restraints generated. 1329 Oldfield, 0 Emsley, 1329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 116 time to evaluate : 0.433 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 462 GLU cc_start: 0.8071 (OUTLIER) cc_final: 0.7466 (mp0) REVERT: A 586 MET cc_start: 0.8965 (OUTLIER) cc_final: 0.8404 (mpp) REVERT: A 609 MET cc_start: 0.8380 (ttm) cc_final: 0.8174 (ttm) REVERT: B 98 LEU cc_start: 0.9398 (OUTLIER) cc_final: 0.9033 (mm) REVERT: B 292 MET cc_start: 0.8145 (ppp) cc_final: 0.7667 (ppp) REVERT: B 586 MET cc_start: 0.8704 (mtm) cc_final: 0.8409 (mtt) outliers start: 27 outliers final: 23 residues processed: 135 average time/residue: 0.0983 time to fit residues: 19.5477 Evaluate side-chains 137 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 111 time to evaluate : 0.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 ILE Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 210 MET Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 442 GLU Chi-restraints excluded: chain A residue 462 GLU Chi-restraints excluded: chain A residue 480 LEU Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 586 MET Chi-restraints excluded: chain A residue 599 VAL Chi-restraints excluded: chain A residue 622 LEU Chi-restraints excluded: chain B residue 72 HIS Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 110 GLU Chi-restraints excluded: chain B residue 279 ASN Chi-restraints excluded: chain B residue 306 VAL Chi-restraints excluded: chain B residue 379 ILE Chi-restraints excluded: chain B residue 390 VAL Chi-restraints excluded: chain B residue 446 LEU Chi-restraints excluded: chain B residue 481 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 537 LEU Chi-restraints excluded: chain B residue 672 ILE Chi-restraints excluded: chain B residue 683 VAL Chi-restraints excluded: chain C residue 146 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 23 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 30 optimal weight: 0.6980 chunk 123 optimal weight: 10.0000 chunk 95 optimal weight: 3.9990 chunk 109 optimal weight: 9.9990 chunk 67 optimal weight: 6.9990 chunk 105 optimal weight: 0.7980 chunk 43 optimal weight: 3.9990 chunk 4 optimal weight: 0.8980 chunk 65 optimal weight: 0.7980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 279 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.114806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.090532 restraints weight = 20970.217| |-----------------------------------------------------------------------------| r_work (start): 0.3245 rms_B_bonded: 2.82 r_work: 0.3036 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8514 moved from start: 0.2269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11035 Z= 0.117 Angle : 0.564 14.155 14892 Z= 0.278 Chirality : 0.041 0.191 1674 Planarity : 0.003 0.054 1889 Dihedral : 5.063 43.887 1540 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 2.12 % Allowed : 15.96 % Favored : 81.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.43 (0.24), residues: 1329 helix: 1.28 (0.23), residues: 537 sheet: 0.53 (0.39), residues: 193 loop : -0.67 (0.27), residues: 599 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 290 TYR 0.043 0.001 TYR C 147 PHE 0.013 0.001 PHE C 146 TRP 0.033 0.002 TRP A 585 HIS 0.004 0.001 HIS B 620 Details of bonding type rmsd covalent geometry : bond 0.00268 (11031) covalent geometry : angle 0.55144 (14886) hydrogen bonds : bond 0.02940 ( 502) hydrogen bonds : angle 4.43363 ( 1488) metal coordination : bond 0.00906 ( 4) metal coordination : angle 5.88756 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2658 Ramachandran restraints generated. 1329 Oldfield, 0 Emsley, 1329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2658 Ramachandran restraints generated. 1329 Oldfield, 0 Emsley, 1329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 113 time to evaluate : 0.392 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 462 GLU cc_start: 0.8065 (OUTLIER) cc_final: 0.7461 (mp0) REVERT: A 586 MET cc_start: 0.8975 (OUTLIER) cc_final: 0.8449 (mpp) REVERT: B 98 LEU cc_start: 0.9394 (OUTLIER) cc_final: 0.9037 (mm) REVERT: B 292 MET cc_start: 0.8084 (ppp) cc_final: 0.7671 (ppp) REVERT: B 586 MET cc_start: 0.8713 (mtm) cc_final: 0.8404 (mtt) REVERT: B 666 GLN cc_start: 0.8794 (tm-30) cc_final: 0.8592 (tm-30) REVERT: C 71 MET cc_start: 0.6418 (ttt) cc_final: 0.5772 (ptp) outliers start: 25 outliers final: 22 residues processed: 132 average time/residue: 0.1007 time to fit residues: 19.3966 Evaluate side-chains 137 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 112 time to evaluate : 0.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 ILE Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 210 MET Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 442 GLU Chi-restraints excluded: chain A residue 462 GLU Chi-restraints excluded: chain A residue 480 LEU Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 586 MET Chi-restraints excluded: chain A residue 599 VAL Chi-restraints excluded: chain A residue 622 LEU Chi-restraints excluded: chain B residue 72 HIS Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 110 GLU Chi-restraints excluded: chain B residue 279 ASN Chi-restraints excluded: chain B residue 306 VAL Chi-restraints excluded: chain B residue 390 VAL Chi-restraints excluded: chain B residue 446 LEU Chi-restraints excluded: chain B residue 481 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 537 LEU Chi-restraints excluded: chain B residue 672 ILE Chi-restraints excluded: chain B residue 683 VAL Chi-restraints excluded: chain C residue 146 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 2 optimal weight: 3.9990 chunk 31 optimal weight: 2.9990 chunk 93 optimal weight: 0.7980 chunk 91 optimal weight: 0.0670 chunk 130 optimal weight: 8.9990 chunk 30 optimal weight: 2.9990 chunk 40 optimal weight: 3.9990 chunk 25 optimal weight: 6.9990 chunk 5 optimal weight: 6.9990 chunk 102 optimal weight: 2.9990 chunk 39 optimal weight: 4.9990 overall best weight: 1.9724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 330 HIS B 279 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.112183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.087681 restraints weight = 21194.769| |-----------------------------------------------------------------------------| r_work (start): 0.3198 rms_B_bonded: 2.85 r_work: 0.2988 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8560 moved from start: 0.2392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 11035 Z= 0.190 Angle : 0.599 14.536 14892 Z= 0.295 Chirality : 0.042 0.190 1674 Planarity : 0.004 0.052 1889 Dihedral : 5.218 45.913 1540 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 2.29 % Allowed : 16.21 % Favored : 81.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.35 (0.24), residues: 1329 helix: 1.19 (0.23), residues: 539 sheet: 0.50 (0.39), residues: 193 loop : -0.71 (0.26), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 290 TYR 0.027 0.002 TYR C 147 PHE 0.014 0.001 PHE C 146 TRP 0.033 0.002 TRP A 585 HIS 0.008 0.001 HIS B 620 Details of bonding type rmsd covalent geometry : bond 0.00439 (11031) covalent geometry : angle 0.58656 (14886) hydrogen bonds : bond 0.03164 ( 502) hydrogen bonds : angle 4.52633 ( 1488) metal coordination : bond 0.01572 ( 4) metal coordination : angle 6.10480 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2013.14 seconds wall clock time: 35 minutes 29.23 seconds (2129.23 seconds total)